NP-MRD: Showing NP-Card for Verdine (NP0070594)

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Record Information

Version

2.0

Created at

2022-04-28 15:59:27 UTC

Updated at

2022-04-28 15:59:27 UTC

NP-MRD ID

NP0070594

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Verdine

Description

(1'S,2R,2'S,3R,3'R,3aS,5'S,6S,7'R,7aR,8'S,10'S,11'S)-3',5',8'-trihydroxy-2',3,6,15'-tetramethyl-3a,4,5,6,7,7a-hexahydro-3H-spiro[furo[3,2-b]pyridine-2,14'-tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]Heptadecan]-15'-en-17'-one belongs to the class of organic compounds known as jerveratrum-type alkaloids. These are steroidal alkaloids with a structure that is based on the jervane ring system. Jerveratrum alkaloids have alkamines with 1-3 oxygen atoms, and occur as such or as monoglycosides. Verdine is found in Veratrum album, Veratrum dahuricum and Veratrum lobelianum . Based on a literature review very few articles have been published on (1'S,2R,2'S,3R,3'R,3aS,5'S,6S,7'R,7aR,8'S,10'S,11'S)-3',5',8'-trihydroxy-2',3,6,15'-tetramethyl-3a,4,5,6,7,7a-hexahydro-3H-spiro[furo[3,2-b]pyridine-2,14'-tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]Heptadecan]-15'-en-17'-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217592D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282217592D          

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 21 22  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  1  6  0  0  0
 21 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 20 27  1  0  0  0  0
 26 28  1  1  0  0  0
 15 29  1  0  0  0  0
 14 30  1  0  0  0  0
  8 30  1  1  0  0  0
 30 31  2  0  0  0  0
  5 32  1  1  0  0  0
  2 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0070594

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1[C@@H]2NC[C@@H](C)C[C@H]2O[C@]11CC[C@H]2[C@@H]3C[C@H](O)[C@@H]4C[C@H](O)C[C@@H](O)[C@]4(C)[C@H]3C(=O)C2=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C27H41NO5/c1-12-7-20-24(28-11-12)14(3)27(33-20)6-5-16-17-10-19(30)18-8-15(29)9-21(31)26(18,4)23(17)25(32)22(16)13(27)2/h12,14-21,23-24,28-31H,5-11H2,1-4H3/t12-,14+,15-,16-,17-,18-,19-,20+,21+,23+,24-,26+,27-/m0/s1

> <INCHI_KEY>
NPWBGQQCCXBLTO-LDUIZNGBSA-N

> <FORMULA>
C27H41NO5

> <MOLECULAR_WEIGHT>
459.627

> <EXACT_MASS>
459.298473424

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
53.011449928337164

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3S,3'R,3'aS,4aR,5S,6'S,6aS,6bS,7'aR,9R,11aS,11bS)-1,3,5-trihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5,5',6,6',6a,6b,7,7',7'a,8,11,11a,11b-icosahydro-3'H-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridine]-11-one

> <ALOGPS_LOGP>
1.26

> <JCHEM_LOGP>
1.178360042333332

> <ALOGPS_LOGS>
-3.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.924387990911761

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.34780614417636

> <JCHEM_PKA_STRONGEST_BASIC>
9.934001326911137

> <JCHEM_POLAR_SURFACE_AREA>
99.02

> <JCHEM_REFRACTIVITY>
125.10259999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.63e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,3'R,3'aS,4aR,5S,6'S,6aS,6bS,7'aR,9R,11aS,11bS)-1,3,5-trihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5,5',6,6',6a,6b,7,7',7'a,8,11a-octadecahydro-3'H-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridine]-11-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      13.580  -0.664   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.541   0.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.979   1.974   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.456   2.204   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.495   1.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.058  -0.434   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.097  -1.637   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.973   1.230   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.411   2.664   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.371   3.868   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.894   3.637   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.855   4.841   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       7.873   2.572   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.485   1.082   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.001   0.673   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.904   1.754   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.292   3.244   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.777   3.653   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.700   2.715   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.415   1.867   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.824   0.382   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.362   0.312   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.210  -0.973   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       1.743  -0.715   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       0.253  -0.327   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.157   1.158   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.925   2.255   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.647   1.546   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.092  -0.864   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.783   0.252   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.874  -1.285   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.535  -0.204   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      16.064   0.310   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    8   32                                             
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9   30                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13    9   14   18                                                  
CONECT   14   13   15   30                                                  
CONECT   15   14   16   29                                                  
CONECT   16   15   17   19   22                                             
CONECT   17   16   18                                                       
CONECT   18   17   13                                                       
CONECT   19   16   20                                                       
CONECT   20   19   21   27                                                  
CONECT   21   20   22   24                                                  
CONECT   22   21   16   23                                                  
CONECT   23   22                                                            
CONECT   24   21   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26   20                                                       
CONECT   28   26                                                            
CONECT   29   15                                                            
CONECT   30   14    8   31                                                  
CONECT   31   30                                                            
CONECT   32    5                                                            
CONECT   33    2                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₁NO₅

Average Mass

459.6270 Da

Monoisotopic Mass

459.29847 Da

IUPAC Name

(1R,3S,3'R,3'aS,4aR,5S,6'S,6aS,6bS,7'aR,9R,11aS,11bS)-1,3,5-trihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5,5',6,6',6a,6b,7,7',7'a,8,11,11a,11b-icosahydro-3'H-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridine]-11-one

Traditional Name

(1R,3S,3'R,3'aS,4aR,5S,6'S,6aS,6bS,7'aR,9R,11aS,11bS)-1,3,5-trihydroxy-3',6',10,11b-tetramethyl-1,2,3,3'a,4,4',4a,5,5',6,6',6a,6b,7,7',7'a,8,11a-octadecahydro-3'H-spiro[cyclohexa[a]fluorene-9,2'-furo[3,2-b]pyridine]-11-one

CAS Registry Number

Not Available

SMILES

C[C@@H]1[C@@H]2NC[C@@H](C)C[C@H]2O[C@]11CC[C@H]2[C@@H]3C[C@H](O)[C@@H]4C[C@H](O)C[C@@H](O)[C@]4(C)[C@H]3C(=O)C2=C1C

InChI Identifier

InChI=1S/C27H41NO5/c1-12-7-20-24(28-11-12)14(3)27(33-20)6-5-16-17-10-19(30)18-8-15(29)9-21(31)26(18,4)23(17)25(32)22(16)13(27)2/h12,14-21,23-24,28-31H,5-11H2,1-4H3/t12-,14+,15-,16-,17-,18-,19-,20+,21+,23+,24-,26+,27-/m0/s1

InChI Key

NPWBGQQCCXBLTO-LDUIZNGBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Veratrum album	LOTUS Database	35616633
Veratrum dahuricum	Plant	KNApSAcK
Veratrum lobelianum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as jerveratrum-type alkaloids. These are steroidal alkaloids with a structure that is based on the jervane ring system. Jerveratrum alkaloids have alkamines with 1-3 oxygen atoms, and occur as such or as monoglycosides.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

Jerveratrum-type alkaloids

Alternative Parents

Substituents

Jerveratrum-type alkaloid
Azasteroid
Alkaloid or derivatives
Piperidine
Cyclic alcohol
Tetrahydrofuran
Ketone
Secondary alcohol
Dialkyl ether
Secondary aliphatic amine
Ether
Oxacycle
Polyol
Azacycle
Secondary amine
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Amine
Organonitrogen compound
Organooxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.26	ALOGPS
logP	1.18	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	14.35	ChemAxon
pKa (Strongest Basic)	9.93	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	99.02 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	125.1 m³·mol⁻¹	ChemAxon
Polarizability	53.01 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10393249

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21769928

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Verdine (NP0070594)

MOL for NP0070594 (Verdine)

3D MOL for NP0070594 (Verdine)

3D SDF for NP0070594 (Verdine)

3D-SDF for NP0070594 (Verdine)

PDB for NP0070594 (Verdine)

3D PDB for NP0070594 (Verdine)

SMILES for NP0070594 (Verdine)

INCHI for NP0070594 (Verdine)

Structure for NP0070594 (Verdine)

3D Structure for NP0070594 (Verdine)